MolNFT v1 · #115569 · protein
Crystal structure of the EGFR kinase domain mutant V924R
5CNO · Epidermal growth factor receptor: “Crystal structure of the EGFR kinase domain mutant V924R”. X-ray diffraction, 2 ligands (ANP, MG), 8 pockets (best druggability 0.80). MolNFT v1 #115569 on GenesisL1: 3D structure, binding sites…
- PDB
- 5CNO
- Type
- protein
- Length
- 612 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Epidermal growth factor receptor
- EC
- 2.7.10.1
- UniProt
- P00533
- Ligands
- ANP, MG
- Pockets
- 8 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 300 | 44% helix, 17% strand | P00533 |
| B | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 302 | 43% helix, 17% strand | P00533 |
| X | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 10 | 0% helix, 10% strand | P00533 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1174 | 0.80 | 0.81 | 93 | ANP, MG |
| 2 | 501 | 0.73 | 0.81 | 59 | ANP, MG |
| 3 | 71 | 0.42 | 0.80 | 15 | empty |
| 4 | 150 | 0.41 | 0.74 | 23 | empty |
| 5 | 92 | 0.40 | 0.77 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–X · 507 Ų buried · 10 hydrogen bonds · protein-protein
- B–X · 463 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 431 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5CNO · Crystal structure of the EGFR kinase domain mutant V924R · the same entry in another collection · chain A against A, TM-score 1.00
- P00533 · AlphaFold monomer V2.0 prediction for epidermal growth factor receptor (P00533) · a predicted model of the same protein · chain A against A, TM-score 0.86
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P00533
- Elsewhere: RCSB PDB 5CNO · PDBe 5CNO · UniProt P00533
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